In the past there were some cases regarding false positives in the Merge feature. If that is the situation, or if you think it's a bug, please submit a brief description in the Submit Feedback tool (menu > Help > Submit Feedback). There should be no difference using the editor from each of those locations.

Regarding the internal editor, you can select other than notepad. Just go to menu Edit > Options > External Editors and point to the one you prefer. My personal option goes to the Free CSS Toolbox which, besides syntax highlighting, provides handy formatting and checking features.

Good luck with your development and let me know if I can help you in anything else.